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BODG_HUMAN_1_387

Gamma-butyrobetaine dioxygenase [Gamma-BBH/TMLD family]

Composition of the binding site

Protein chains monomer
A1 (BODG_HUMAN):176:179, 181, 183, 186, 191:194, 199, 202, 204:206, 217, 229, 292, 295, 338, 340, 347:349, 360, 362, 366176:179, 181, 183, 186, 191:194, 199, 202, 204:206, 217, 229, 292, 295, 338, 340, 347:349, 360, 362, 366
Metals (Me):Ni/Zn

Full PDB list

3ms5, 3n6w, 3o2g, 4bg1, 4bgk, 4bgm, 4bhf, 4bhg, 4bhi, 4c5w, 4c8r, 4cwd

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Y
1
7
7
W
1
8
1
V
1
8
3
N
1
9
1
A
1
9
3
Y
1
9
4
L
1
9
9
H
2
0
2
D
2
0
4
Y
2
0
5
P
2
0
6
L
2
1
7
S
2
2
9
N
2
9
2
T
2
9
5
F
3
4
0
H
3
4
7
G
3
4
8
R
3
4
9
R
3
6
0
L
3
6
2
Y
3
6
6
[1]3ms5.a oga,ree20 . . . . . . . . . . . . . . . . . . . . . . Ni
[1]3n6w.a none . . . - - - . . . . . . . . . . . . . . . .
[1]3o2g.a nm2,oga20 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4bg1.a ivl,oga22 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4bgk.a oga,rtk20 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4bgm.a dlt,oga22 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4bhf.a mzt,oga21 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4bhg.a c2t,oga21 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4bhi.a oga,ruj21 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4c5w.a nm3,oga20 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4c8r.b 6yt23 . . . . . . . . . . . . . . . . . . . . . . Ni
[1]4cwd.a 449,oga21 . . . . . . . . . . . . . . . . . . . . . . Ni

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1 Me
F
1
7
6
Y
1
7
7
G
1
7
8
H
1
7
9
W
1
8
1
V
1
8
3
K
1
8
6
N
1
9
1
V
1
9
2
A
1
9
3
Y
1
9
4
L
1
9
9
H
2
0
2
D
2
0
4
Y
2
0
5
P
2
0
6
L
2
1
7
S
2
2
9
N
2
9
2
T
2
9
5
I
3
3
8
F
3
4
0
H
3
4
7
G
3
4
8
R
3
4
9
R
3
6
0
L
3
6
2
Y
3
6
6
[1]3ms5.a . . . . . . . . . * . . . . . . . . . . . . . . * . . . Ni
[1]3n6w.a . . . . . . . - - - - . . . * . . . . . . . . . . . . .
[1]3o2g.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . Zn
[1]4bg1.a . . . . . . . . . * . . . . . . . . . . . . . . * . . . Zn
[1]4bgk.a . . . . . . . . . * . . . . . . . . . . . . . . * . . . Zn
[1]4bgm.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . Zn
[1]4bhf.a . . . . . . . . . * . . . . . . . . . . . . . . * . . . Zn
[1]4bhg.a . . . . . . . . . * . . . . . . . . . . . . . . * . . . Zn
[1]4bhi.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . Zn
[1]4c5w.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . Zn
[1]4c8r.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ni
[1]4cwd.a . . . . . . . . . * . . . . . . . . . . . . . . * . . . Ni

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3ms5.a:oga,ree
3n6w.a is apo
3o2g.a:nm2,oga
4bg1.a:ivl,oga
4bgk.a:oga,rtk
4bgm.a:dlt,oga
4bhf.a:mzt,oga
4bhg.a:c2t,oga
4bhi.a:oga,ruj
4c5w.a:nm3,oga
4c8r.b:6yt
4cwd.a:449,oga
[1] 3ms5.a
0
- 0 0.1 0 0 0 0.2 0 0 2.9 0.1
[1] 3n6w.a 1.6
-
1.9 2.4 3.1 1.9 2.6 3.0 3.0 1.5 0.4 3.1
[1] 3o2g.a 0 -
0
0.1 0 0 0 0.2 0 0 3.0 0
[1] 4bg1.a 0 - 0
0
0 0 0 0 0 0 3.6 0
[1] 4bgk.a 0.1 - 0.2 0
0
0 0 0 0 0 3.9 0.1
[1] 4bgm.a 0 - 0 0 0
0
0 0 0 0 3.4 0
[1] 4bhf.a 0 - 0 0 0 0
0
0 0 0 3.6 0
[1] 4bhg.a 0.1 - 0.2 0 0 0 0
0
0 0 3.7 0.1
[1] 4bhi.a 0 - 0 0.1 0 0 0 0.1
0
0 3.1 0
[1] 4c5w.a 0 - 0 0 0 0.1 0 0 0
0
3.1 0
[1] 4c8r.b 0.2 - 0.1 0 0.1 0.1 0.1 0.2 0.2 0
0.3
0.1
[1] 4cwd.a 0.1 - 0 0.1 0 0.2 0 0.1 0 0.1 3.2
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3ms5.a
3n6w.a
3o2g.a
4bg1.a
4bgk.a
4bgm.a
4bhf.a
4bhg.a
4bhi.a
4c5w.a
4c8r.b
4cwd.a
[1] 3ms5.a
0
.20 .01 .04 .07 .04 .04 .05 .02 .03 .11 .04
[1] 3n6w.a .20
0
.20 .21 .22 .20 .21 .21 .20 .19 .11 .20
[1] 3o2g.a .01 .20
0
.03 .06 .03 .03 .04 .01 .02 .11 .03
[1] 4bg1.a .04 .21 .03
0
.03 .02 0 .02 .02 .02 .12 .02
[1] 4bgk.a .07 .22 .06 .03
0
.02 .03 .01 .04 .04 .14 .05
[1] 4bgm.a .04 .20 .03 .02 .02
0
.02 .01 .03 .03 .12 .03
[1] 4bhf.a .04 .21 .03 0 .03 .02
0
.02 .02 .02 .12 .02
[1] 4bhg.a .05 .21 .04 .02 .01 .01 .02
0
.04 .04 .13 .04
[1] 4bhi.a .02 .20 .01 .02 .04 .03 .02 .04
0
.01 .12 .03
[1] 4c5w.a .03 .19 .02 .02 .04 .03 .02 .04 .01
0
.11 .02
[1] 4c8r.b .11 .11 .11 .12 .14 .12 .12 .13 .12 .11
0
.10
[1] 4cwd.a .04 .20 .03 .02 .05 .03 .02 .04 .03 .02 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3ms5.a
3n6w.a
3o2g.a
4bg1.a
4bgk.a
4bgm.a
4bhf.a
4bhg.a
4bhi.a
4c5w.a
4c8r.b
4cwd.a
[1] 3ms5.a
0
4.0 0.1 0.2 0.3 0.2 0.2 0.3 0.2 0.2 7.2 0.2
[1] 3n6w.a 4.0
0
4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.1 4.0
[1] 3o2g.a 0.1 4.0
0
0.2 0.2 0.2 0.1 0.2 0.1 0.1 7.3 0.1
[1] 4bg1.a 0.2 4.0 0.2
0
0.2 0.1 0.1 0.2 0.1 0.1 7.2 0.2
[1] 4bgk.a 0.3 4.0 0.2 0.2
0
0.2 0.1 0.1 0.1 0.1 7.2 0.2
[1] 4bgm.a 0.2 4.0 0.2 0.1 0.2
0
0.1 0.2 0.1 0.1 7.2 0.2
[1] 4bhf.a 0.2 4.0 0.1 0.1 0.1 0.1
0
0.1 0.1 0.1 7.3 0.1
[1] 4bhg.a 0.3 4.0 0.2 0.2 0.1 0.2 0.1
0
0.1 0.1 7.3 0.2
[1] 4bhi.a 0.2 4.0 0.1 0.1 0.1 0.1 0.1 0.1
0
0.1 7.3 0.1
[1] 4c5w.a 0.2 4.0 0.1 0.1 0.1 0.1 0.1 0.1 0.1
0
7.3 0.1
[1] 4c8r.b 7.2 4.1 7.3 7.2 7.2 7.2 7.3 7.3 7.3 7.3
0
7.3
[1] 4cwd.a 0.2 4.0 0.1 0.2 0.2 0.2 0.1 0.2 0.1 0.1 7.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3ms5.a
3n6w.a
3o2g.a
4bg1.a
4bgk.a
4bgm.a
4bhf.a
4bhg.a
4bhi.a
4c5w.a
4c8r.b
4cwd.a
[1] 3ms5.a
0
5.3 0.2 0.4 0.6 0.6 0.5 0.5 0.5 0.5 7.2 0.5
[1] 3n6w.a 5.3
0
5.2 5.2 5.2 5.2 5.2 5.2 5.2 5.2 5.5 5.2
[1] 3o2g.a 0.2 5.2
0
0.4 0.5 0.5 0.5 0.5 0.5 0.5 7.2 0.5
[1] 4bg1.a 0.4 5.2 0.4
0
0.4 0.3 0.3 0.2 0.3 0.4 7.2 0.4
[1] 4bgk.a 0.6 5.2 0.5 0.4
0
0.2 0.2 0.3 0.2 0.3 7.2 0.2
[1] 4bgm.a 0.6 5.2 0.5 0.3 0.2
0
0.2 0.4 0.1 0.2 7.2 0.2
[1] 4bhf.a 0.5 5.2 0.5 0.3 0.2 0.2
0
0.3 0.1 0.2 7.2 0.2
[1] 4bhg.a 0.5 5.2 0.5 0.2 0.3 0.4 0.3
0
0.3 0.4 7.2 0.4
[1] 4bhi.a 0.5 5.2 0.5 0.3 0.2 0.1 0.1 0.3
0
0.2 7.2 0.2
[1] 4c5w.a 0.5 5.2 0.5 0.4 0.3 0.2 0.2 0.4 0.2
0
7.2 0.3
[1] 4c8r.b 7.2 5.5 7.2 7.2 7.2 7.2 7.2 7.2 7.2 7.2
0
7.3
[1] 4cwd.a 0.5 5.2 0.5 0.4 0.2 0.2 0.2 0.4 0.2 0.3 7.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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